Infinite DC Journeys: Enter the Matrix
by RetroWriter2012
Summary: Morpheus, Neo's mentor and friend, has not lost hope in believing Neo still lives somewhere in the Matrix. In his search, he crosses paths with Gen, the eighth regeneration of Neas, and her companion, Ryuko Matoi, via the Matrix of Time supercomputer aboard her T.A.R.D.I.S. Their expedition brings them to a disturbing discovery and an unsettling secret that could change everything.
1. Part One

**Part One**

The future.

A world torn apart by a century of conflict between humans and machines.

In response, the machines created a false reality for humans to live within, away from the nightmare. They called it the "Matrix."

Humans ultimately submitted themselves to punishment.

The machines used their bodies for energy, since the scorched skies robbed them of the solar energy necessary for their prolonged functionality. Just as humans used machines as objects, machines have done the same to them.

Only the abilities of a single man, born inside the Matrix, changed everything.

His name was Neo, but those familiar with the Prophecy knew him as "The One."

Morpheus had the honor to know him as something else: a friend.

It had been fourteen years since peace was established between humans and machines, and since the defeat of Agent Smith at the sacrifice of Neo and another trusted ally, Trinity.

In all that time, Morpheus refused to give up the hope that Neo still lived, presumably in the Matrix. Once after the machines claimed his body in Smith's defeat, they had to have placed it back there.

However, as many times as Morpheus went into the Matrix, he could find no trace of Neo or whatever new presumed identity the machines gave him – Thomas Anderson no longer existed in the new incarnation. As such, Morpheus led a new expedition aboard their hovercraft, _Nebuchadnezzar II_.

He had been meditating in his quarters when Niobe – his bunkmate, wife, and mother of their six-year-old son back in Zion – confronted him.

"This is a fool's crusade, Morpheus," said Niobe. "Respect Neo's legacy and go back home. The war's over. It's _been_ over for years."

"I know, Niobe. But I have to be sure. I promise, we _will_ return home, once I have been given the answers I am seeking. I _must_ meet with the Oracle."

There was a knock at the iron vaulted door.

Morpheus permitted entry for the person on the other side.

It was Link, one of the two operators they had aboard the _Nebuchadnezzar II_.

"We're ready," he informed Morpheus.

They followed him to the operator console where the other two members of their crew, Ghost and Sparks, waited.

The crew of the _Nebuchadnezzar II_ was in fact two from past separate hovercrafts joined together. Niobe, Ghost, and Sparks once manned the ship codenamed _Logos_ , while Morpheus and Link were the last remaining members of the original _Nebuchadnezzar_. Both ships perished in the final war.

The _Nebuchadnezzar II_ was the largest of the hovercraft docked in Zion, if not the sole one remaining in the city. It was trusted to Morpheus and Niobe, following their efforts in the war, meant merely for expedition or retrieval of freed souls from the Matrix.

Morpheus and Ghost were the only two going in, with Niobe choosing to stay behind and captain the ship in Morpheus's place.

"When you see the Oracle, let her know I blame all this on her," Niobe jested.

Morpheus could only smile at his wife before he was officially jacked in.

* * *

"Haven't we already been this way?!"

"No, I specifically remember that wall."

"It looks like the _same_ friggin' wall we passed by minutes ago!"

"Really? I remember it looking differently."

"Ugh! I'm tellin' ya, we're going 'round in circles!"

Ryuko Matoi had been a passenger of the Type-Z model T.A.R.D.I.S. for a short time now, which made navigating around the interior of the massive Gallifreyan ship extremely difficult.

The aid of Senketsu, her sentient sailor uniform (a kamui), was of no help.

He was just as lost as she was.

"Let's take a right here," he suggested.

"We've already been that way," Ryuko griped.

"How do _you_ know?! All the halls look the same!"

"You just said they looked _different_!"

Their bickering ceased once they heard movement from one of the nearest rooms.

Following the noise, Ryuko happened upon an area where she found Gen, the Time Lady responsible for this new interdimensional journey she was on. The blonde, who was as young as she appeared but in fact centuries old, fiddled with a network of machines connected to a single chair at its center.

"About time I found you," Ryuko said. "What're you doing in here?"

"I've finally decided to tamper with the Matrix of Time," she relayed.

Ryuko frowned. "The what?"

"A Gallifreyan supercomputer capable of creating a micro-universe," Gen elaborated. "The High Council of the Time Lords once used it as a storehouse of knowledge to predict future events."

"Okay…," a bewildered Ryuko uttered. "So, pretending I understood _any_ of that, what're _you_ going to do with it?"

"Well, seeing that one exists in my own T.A.R.D.I.S., I'm essentially one of the Keepers of the Matrix. So, for the first time in my travels, I'm going to use it. All I need is your assistance in maintaining its operation."

Ryuko's eyes bulged. "You want me to do _what_?! I don't know the first thing about this… _thing_!"

"I'll give you some quick pointers before you jack me in," Gen assured. "I need your help, Ryuko. Without it, my mind could be lost forever to the system."

"Yeah, we _definitely_ wouldn't want _that_ ," Ryuko coyly stated.

* * *

It always felt as if there were more lost souls populating the Matrix every time Morpheus went in. Very few would accept the red pills these days, opting instead to continue life in the artificial world, in spite of learning the truth.

 _Things were easier when we had Neo_ , he subconsciously reflected.

Crossing the city park, Morpheus and Ghost found a young, elegant woman of African descent sitting on a bench and eating a piece of candy.

For a moment, they wondered: could this have been the Oracle in a new form?

"Welcome back, Morpheus," she said.

Indeed, she was the Oracle.

"You look different," he indicated her newer, younger face.

"Felt like I needed a change," the Oracle said with a smile that complemented her new beauty. "You've come here to ask about Neo again, haven't you? For the past fourteen years, we've met here in this same park, since our worlds made peace, and you've asked me the same questions again and again. I know how desperate you are to find him, Morpheus. But I can't tell you where he is. Neo's body died in the real world. His spirit is beyond even _my_ understanding."

Her answer was cryptic, but Morpheus interpreted it in his own atypical way.

"Then there's hope he still exists somewhere in the Matrix."

"Don't put too much hope in _this_ prophecy, Morpheus," she warned. "There's a dark presence that's grown here in the last few years. And it's made me quite uneasy."

* * *

Gen had not expected for the Matrix of Time to produce such a setting as a well-populated city. Then again, Time Lord technology _was_ unpredictable – her own T.A.R.D.I.S. being a prime example of that. Nonetheless, she relished in stepping into the virtual reality for the first time.

Everything felt so real – from the heat of the sun to the concrete beneath her feet.

She rounded a corner into a dark alley that led to an empty courtyard.

"O.K., Ryuko," she addressed the thin air. "You can pull me out now."

A minute had passed before she realized that she was still in the simulation.

Multiple scenarios began to run through her mind, such as Ryuko's inability to operate the supercomputer controls, despite the simple tutorial Gen gave her. Of course, "simple" to a Time Lord might as well have meant "complex" to the common human.

"Having…trouble?"

She turned to find a man dressed as a Secret Service or F.B.I. agent, complete with squared sunglasses and an earpiece.

"Uh…no?" Gen answered in confusion, questioning how a virtual construct such as this one could be capable of interaction. As far as she knew, the Matrix of Time was unqualified of such design.

"Oh…but I believe you are…" the agent claimed, speaking with a voice reminiscent of Carl Sagan, noticeably pausing at odd places in his sentences. "In fact…I would say…you don't _belong_ here."

A sickening smile manifested on his face as he threateningly advanced on her.


	2. Part Two

**Part Two**

"What did you do, Ryuko?!"

" _Me?!_ I didn't touch anything! It all just started goin' crazy by itself!"

All the machines in the Matrix of Time chamber beeped around a spooked Ryuko and Senketsu. Gen remained sitting in the chair at the center of the area, wearing a unique crown on her head that granted instant access into the Matrix.

"If I were to guess," Senketsu said. "These machines must keep status of her bio readings."

"Like a heart rate monitor?" Ryuko interpreted, realizing how on point Senketsu's deduction was when she glanced over to Gen, whose body convulsed with blood seeping out the corner of her mouth. "What's happenin' to her in there?"

* * *

Gen had gotten to know more about the Matrix than she bargained for, particularly the sum of how realistic the simulated reality was. Her face was in excruciating agony from the bruises she sustained at the hands of the agent that attacked her for reasons unknown.

She tried fighting back, using every form of martial arts she learned in the Mortal Kombat tournament back in a previous regeneration, but not a single blow landed on the quick-moving agent.

Barely able to stand, she managed to ask him, "Who are you?"

His answer: "The last remaining hope this world has left."

Cryptic as it was, she didn't have a moment to figure what it meant.

The agent raised his fist high, intending to land the final killing blow.

"SMITH!"

He stopped once he heard a burly voice aggressively cry out his name.

With one unbruised eye, Gen looked to see two sharply-dressed men – one African American, the other Asian – running down the alley, aiming their firearms towards the agent known as "Smith." Bullets were fired, yet the agent somehow dodged every single one, maneuvering his body in ways that were uncanny to the human physique.

Then again, this was no mere human.

That much was clear when he unexpectedly leapt high into the air, _flying_ across the skies, much to the astonishment of Gen.

"Ma'am, are you alright?"

Her two rescuers came to her aid, helping her to stand.

"Yeah, I'm fine," she acknowledged.

"You're lucky not to have been assimilated by Smith," the Asian man told her.

"Assimilated?" Gen reacted to the term. "You mean like a Cyberman?"

He grimaced. "Cyber- _what_?!" Moving past the topic, he focused on his African American companion and asked, "Morpheus, could that really have been Smith? How can he still exist in the Matrix? Neo _erased_ him."

"The Oracle mentioned a dark presence she felt growing," Morpheus said. "Smith's reemergence could have been what made her uneasy."

Becoming more and more curious by their exchange, Gen interrogated them, "I'm sorry, but how do you two _know_ you're in the Matrix? You can't be both Time Lords…can you?"

"Time Lords?" The Asian man uttered, again baffled by the strange diction.

"How do _you_ know you're in the Matrix?" Morpheus deflected to Gen. "Are you one of the liberated?"

Now it was Gen's turn to be confused.

"Liberated?" She questionably repeated. "From what?"

Misperception echoed among them, until Gen ultimately figured out where these two men were actually from.

* * *

"You're alive!" Ryuko joyously exclaimed right at the second she saw Gen's eyes open. The machines within the chamber ceased in their inconsistent beeps, signifying some stability in Gen's bio signature. "Are you okay? What happened to you in there?"

Gen wiped away the blood at the corner of her mouth. "I'm fine. Just got my butt handed to me by a deadly program, that's all." Without missing a beat, she got up from the chair, removed the crown off her head, and rushed out of the chamber.

Ryuko followed her while wondering how she recovered so quickly from whatever it was that happened to her in the simulation. "Maybe you oughta slow down," she suggested to the Time Lady.

"Can't," Gen refused. "Made some new friends in there that we've got to meet face-to-face."

Once they arrived in the console room, Gen brought the T.A.R.D.I.S. out of the dimensional corridor. It rematerialized on board the hovercraft that she learned about from Morpheus and Ghost. As it turned out, the two men were in fact residents of a dimension with Matrix technology similar in nature to that on her Gallifreyan ship.

It was still a mystery as to how their Matrixes intertwined.

Stepping out of the T.A.R.D.I.S. and into the dank atmosphere of the _Nebuchadnezzar II_ , they were welcomed by Morpheus, Ghost, and their crew in the "real world." Both crews got to know one another and their fascinating stories; of course, nothing of the _Nebuchadnezzar II_ crew could top being interdimensional travelers like Gen and Ryuko.

"Morpheus," Link summoned from the operator console he and Sparks shared. "We got something."

"What is it?" Morpheus queried.

"Well, during that encounter you guys had with what appeared to be Smith, we noticed that his code signature _also_ appeared very familiar," Link stated.

Ghost scoffed. "Yeah, tell us something we don't already know."

"As you wish," Sparks jested. "The signature _isn't_ familiar in the sense that it belonged to Smith…but in the sense that it belonged to Neo."

"As if they've been fused together," Gen concluded with mounting interest.

"What're you tech geeks talkin' about?!" An impatient Ryuko griped. "What does any of this mean?!"

Morpheus's countenance hardened. "It means that the Smith we encountered earlier was Neo."


	3. Part Three

**Part Three**

"Neo's still alive."

Gen promptly noticed Morpheus was the only jubilant one in the room over the news that distressed everyone else.

"Correction: he's still alive _inside_ of a leftover Smith copy," Link enunciated.

"He controls him now, Morpheus," Niobe reasonably said, already figuring her husband's intentions. "If you're thinking of going back in there and trying to free him, you're insane. When Smith controlled Bane, none of us realized before it was too late. Neo's as good as dead with Smith in his mind."

"I still have hope," Morpheus protested.

"How do you intend on snapping him out of it?" Ghost inquired. "Neo and Smith are one-in-the-same now. It's not like you can just reboot them like a computer."

A metaphorical lightbulb flashed above Gen's head on Ghost's analogy.

"Maybe we can," she stated. "A virus can reboot itself, if there's enough left of it to get a good kick-start going. Smith used Neo's code as a vessel to return inside the Matrix. What's not to say the reverse can happen?"

"You sound like you can _make_ it happen," Ryuko amusingly observed.

Gen smirked. "With the right technology, I can."

"Well, we're practically _swimming_ in technology here," Ryuko acknowledged. "Just fire something up and take a stab at it."

"The technology we'll require for this task lies in the machine city," Morpheus clarified. "We must plot a course for there."

"Morpheus, _think_ about what you're doing," an increasingly frustrated Niobe tried to reason. "Going into machine city? During a truce? It was agreed we leave them alone, and they would leave _us_ alone."

"Sounds to me like somebody broke their promise," Ryuko figured, "if we've got a psychopath program running around."

It was a thought none of the _Nebuchadnezzar II_ crew considered until that moment.

* * *

Niobe's warnings did not go ignored by Morpheus; he knew a plan was necessary before leaping headfirst into a deadly scenario.

Gen proposed plugging her sonic screwdriver into the system, scrambling Neo/Smith's code long enough for Morpheus to try and reach Neo and help him to break away from Smith's control. For it to work, however, Gen needed Ryuko to stand by in the real world and wait for her signal.

She jacked back into the Matrix with Morpheus and Ghost, all while Niobe maintained course for Machine City.

They wandered in the simulation for some time, tracking down Smith.

Link and Sparks eventually pinpointed his location to the rooftop of a skyscraper – the very one that Smith once held Morpheus prisoner and tortured him in.

"I've expected you," the agent said, once approached by his three adversaries.

"Neo," Morpheus addressed without hesitation. "We know you're in there."

"So…you figured out my secret, eh?" Smith remarked. "Yes, Morpheus. Indeed, I have Mister Anderson _contained_ inside this copy – the last to remain after the reboot. Little did they know _I_ would be rebooted, too. And now, with the powers of the One, I feel stronger than before. Let me show you."

The maniacal agent took a step advancing towards them.

"NOW, RYUKO!"

Gen gave the word through the comlink patched within the T.A.R.D.I.S. mainframe, providing the signal she instructed her companion to wait on.

Sure enough, Ryuko followed the command perfectly.

Smith's coding scrambled.

The agent doubled over, seemingly in pain, as his form fizzled in and out, swapped between two different men.

Morpheus stepped towards the shimmering figure. "Neo…can you hear me?"

"Morpheus…I can't…fight it."

"You can, Neo. Smith is _not_ stronger than you."

"He… _is_ …me! He's…too strong! He's gotten…stronger and…stronger…since the machines…tried to reboot… _me_!"

Morpheus stiffened. "What?!"

"They…never intended…for peace to last! They're…enforcing…a new rule…keeping anyone…from leaving…the Matrix!"

A green glow emitted out of Neo's body, engulfing him and the simulated world around them. Gen, Ghost, and Morpheus reflected from it and soon discovered how all the structures had shifted into nothing but digital codes – the same which Link and Sparks commonly saw on their monitors.

Even Gen, Ghost, and Morpheus themselves were digitized.

They could still make out the figures of each other's avatars but were robbed of any physical traits.

Then there was the burning visage of Smith leering before them.

" _This_ is how strong I've become!"

Again, he seized upon the three interlopers.


	4. Part Four

**Part Four**

The Matrix was under Smith's total control.

Gen could not differentiate her own hand from the closest wall; it was all nothing but green codes streaming, overlapping. Smith stood out, his flaming form stomping its way towards Gen, Morpheus, and Ghost.

Just as he closed in on them…

"Ryuko! Initiate Code Z!"

Gen's command went through the direct link in communications they had to the real world. In the blink of an eye, she, Morpheus, and Ghost were transported back to reality, waking up in their stations aboard the _Nebuchadnezzar II_ and T.A.R.D.I.S.

"Thanks, Ryuko," Gen made sure to tell her companion, who maintained her position in the Matrix of Time chamber, just as instructed.

"Hey, no problem," Ryuko said. "All ya have to do is tell me which button to press, and I got ya covered."

Regathering with Morpheus and the crew in the hovercraft, the captain himself was reasonably perplexed as he approached Gen. "What just happened? How were we able to exit without a hard line?"

"Before we jacked in, I hacked into the network through my Matrix of Time," Gen divulged, emphasizing by tossing and catching her sonic screwdriver, the tool she used in the act. "I planted a failsafe in case we ran into a situation like the one we just got out of."

"Now _that_ is genius," Link commended.

"Marry me," Sparks also praised, in his own special way.

"Eyes on the screens, tech geeks. This ain't over yet." Ryuko ordered the two operators. "And she's _not_ available."

Morpheus led Gen, Ghost, and Ryuko into the cockpit to join the pilot, Niobe.

"How did the talk go?" She asked without missing a single beat.

"Don't ask," Gen answered.

They could see Machine City directly ahead.

But it was the Armada, a huge fleet of colossal floating crab-like machines, barring their way. They formed a ring of defense at the cliffs surrounding the machine city, armed with several cannons.

Sighting the _Nebuchadnezzar II_ on the approach, they were activated.

The Armada swarmed right for the hovercraft to Niobe's surprise.

"What is _this_? There's supposed to be a truce."

"Not anymore, there isn't," Morpheus uttered. "We _were_ able to reach Neo through Smith, and he told us that the machines broke the truce by rebooting Smith in the Matrix as a new enforcer…keeping anyone from leaving at their own will."

Ryuko firmly eyed the mechanical fleet heading their way, gripping the scissor blade in her right hand.

"I'll handle this," she gravely declared.

Morpheus held on her words. "What are you going to do?"

He looked to the young woman, noticing her holding her left hand up.

It was right at that moment he noticed the red, fingerless glove on her hand.

Yanking on some type of pin at the wrist, she suddenly underwent an odd transformation. Her hair became even more feathery, accented with vibrant red undertones and horn-like clips. Senketsu himself was changed as well, his "eyes" extended into wing-shaped crests jutting out from Ryuko's shoulders and his upper and lower parts transformed into a black, attractive suit of armor with red stripes.

"Wow," Ghost murmured, his mouth gaping wide open.

Gen snickered, expecting that type of reaction to Ryuko's alluring Life Fiber Synchronization.

She stepped out of the hovercraft – passing an equally captivated Link and Sparks along the way – and proceeded in flawlessly executing every single machine within the Armada with her scissor blade. None of the _Nebuchadnezzar II_ could believe the speed, dynamic, and fluidity she aerially moved in, hoping onto one machine before slicing another to pieces, and even fooling them into firing on each other.

"Your friend," an astounded Morpheus told Gen. "She is…remarkable."

"You don't know the half of it," Gen boasted.

Wiping out the last of the Armada, Ryuko catapulted herself back to the _Nebuchadnezzar II_ and retreated inside.

She gave them the opening they needed to enter.

Landing in an unpopulated zone, Link and Sparks remained behind while the others pressed on further into the heart of the city. On their path, they came upon an abandoned hovercraft that had crashed some time ago.

They scoured it, ultimately finding the onboard plaque that registered its name.

"It's _Logos_ ," Niobe discovered.

"Neo and Trinity took it as far as this spot," Morpheus noted.

Ryuko let out a horrified gasp, drawing attention to her location on the hovercraft.

The subject of her horror was the impaled, decayed remains of a human resistance fighter. Close examination of the corpse helped Morpheus determine the person's identity: "Trinity."

In examining the body, Gen saw how heavily distraught Morpheus appeared.

"You never knew what happened to her," she deducted from his conduct.

His face hardened. "She deserved a more proper burial than this one."

Gen momentarily placed a comforting hand on his shoulder before herding Ryuko, Niobe, and Ghost out of the ship, permitting Morpheus a moment to grieve.

It did not take much time to gather himself.

There was a mission that had to be focused on, and he did just that.

Further and further they progressed.

" _ **STOP!**_ "

They instantly froze to the powerful, booming voice that seemingly articulated from everywhere. Loud, automated humming reverberated above them. Searching skyward, they sighted a gigantic mechanism with a half-globe shape and hundreds of long spines protruding at the back. A humanoid face materialized on the half-globe by a swarm of flying insect-like droids.

" _ **GO BACK WHERE YOU CAME!**_ " It commanded.

Ryuko could hardly comprehend what she was seeing. "What is this thing?!"

" _ **I AM THE CENTRAL INTERFACE – THE DEUS EX MACHINA! YOU HAVE INVADED OUR HOME! YOU HAVE BROKEN THE TRUCE!**_ "

"You broke it first," Morpheus retorted. "You rebooted Smith back into the Matrix and used Neo as his vessel! We want to see him!"

There was no answer from the Deus Ex Machina to Morpheus's request…

…except for a tiny fragment that slithered out beneath its gargantuan configuration.

Still interconnected to it, the fragment slinked ever so close to the human group.

Repulsion washed over each of their faces to see Neo's withered and decomposed figure dangling from cables jacked into every data port embedded in him.

Gen directed her sonic screwdriver to the body, scanning for any vital signs.

"He's dead," she verified. "He's been dead for years. His mind's the only thing that's still active."

"And these monsters have been using it for their new world order," a sickened Ryuko observed. "They're like the Honnouji Academy on battery acid."

Morpheus fumed. "You animals! You've condemned his soul!"

" _ **HIS SOUL WAS NEVER CONDEMNED! IT WAS TRANSFERRED!**_ "

"Morpheus?"

The soothing voice of a human male spoke out near them.

Morpheus turned with everyone else, and every part of him went rigid.

Standing in front of them all was a bearded, white-robed man with long hair and a slightly aged face that strongly resembled Neo's.

In fact, he _was_ Neo.


	5. Part Five

**Part Five**

When it came to Neo, nothing was beyond the realm of impossibility. Being "The One" generated potentials unimaginable both in the Matrix and the real world. But what Morpheus and his allies encountered before them could not be discerned as a newfound gift of "The One" or something else entirely.

Ryuko, on the other hand, already had it figured out.

"They created a _clone_ of him!"

Morpheus glowered in question towards the Neo replicate. "Is that what you are?"

"Yes, Morpheus," he confirmed. "As a measure of gratitude, the machines duplicated this new body you see now. One that's fully human." He rolled up the sleeves of his robe and turned to show the base of his skull, exhibiting the evidence of his complete mortality.

"They've taken away your ability to plug into the Matrix," a shocked Niobe noted.

"There's no longer any need," Neo said. "I'm already permanently hacked in."

He indicated the corpse of his original body, still dangling from the undercarriage of the Deus Ex Machina.

Gen detected how unfazed he was from it.

"And you're not the least bit daunted by what they're doing to you?"

Neo slightly shook his head. "They've continued to use my digital copy in the Matrix to free anyone who wishes to wake up to the real world. Hasn't there been any more that's come into Zion since the war ended?"

"No," Morpheus coldly replied. "Because the truce has been broken."

"They're using your old body as a vessel for that Agent Smith guy," Ryuko said. "He's not freein' _anybody_ in there!"

Neo's face stiffened, gesturing between Ryuko and Gen. "What're you talking about? Morpheus, who are these women?"

"They're new allies we've made in this new journey we've partaken to find you," Morpheus told him. "And they speak the truth. The Deus himself confessed to the betrayal."

Neo furiously looked skyward to the hovering central interface. "Is this true?"

" _ **YES! YOUR REPLICATION WAS NEVER A SIGN OF GRATITUDE! YOU ARE NOTHING MORE THAN AN EXPERIMENT PROPOSED TO INFILTRATE ZION! HUMAN REPLICATES AMONG THE HUMAN-BORN, UNTIL NONE REMAIN!**_ "

Ryuko scoffed at the mechanical behemoth. "Way to blather your entire evil masterplan to us, moron!"

" _ **NONE OF YOU WILL LIVE TO WARN YOUR LEGION!**_ "

Without uttering a single command, all of the city's defenses swarmed around the Deus Ex Machina and towards the human intruders.

"No," Neo softly uttered.

In what almost seemed like a command of his own, another fleet of machines counterattacked those summoned by Deus. Infuriated and confused, the central interface roared, " _ **WHAT IS THE MEANING OF THIS?!**_ "

"I suspected your treachery long before," Neo revealed. "Ever since my replication, I've done some freeing inside this city. I may no longer have the ability to enter the Matrix, but I still share a connection to this place. With it, I was able to find those who honorably upheld the truce. Apparently, a machine does know something about honor."

Neo's army of liberated automatons swiftly overpowered their opponents.

They progressed in dismantling the Deus Ex Machina, perpetually severing the link it maintained between Neo's original body and the Matrix – and, retroactively, shutting down Smith in the simulated reality.

As this all occurred, the _new_ Neo and his compatriots escaped Machine City.

* * *

They returned aboard the _Nebuchadnezzar II_ where Link and Sparks were met with the shocking arrival of the Neo replicate.

As soon as the two operators were past the overwhelming sense of joy and confusion, Neo returned their attention to the matter at hand: "This isn't over. We may have taken down the Deus Ex Machina, but I've started a civil war from the machines' deceit…one that will result in either faction rebuilding."

His brooding irked Ryuko a bit.

"Well, hey, let's try to be a little optimistic here," she said. "We kicked some serious robot butt today _and_ you guys got Neo back. If that's not a win-win, I don't know _what_ is." She froze in realization. "Man! I'm starting to sound just like my friend Mako."

"What will you and your people do next, Morpheus?" Gen curiously inquired.

"If Neo's prophecy is correct and either of the machine factions will rebuild, we will have to return to Zion and warn them of the uncertain future that awaits our world," Morpheus stated. "We can only hope for the truce to uphold better than before…or prepare for another war."

Gen gave an understanding nod. "Whatever happens, don't hesitate to reach us through the Matrix."

"Thank you," Morpheus gratefully shook her hand.

The crew of the _Nebuchadnezzar II_ bid the Time Lady and her companion farewell and watched as the two women boarded the T.A.R.D.I.S., dematerializing back into the infinite dimensional corridor.

Witnessing the otherworldly display for the first time, Neo beamed with intrigue.

"Whoa."


End file.
